biolmai 0.2.3__tar.gz → 0.2.5__tar.gz

biolmai-0.2.5/PKG-INFO

@@ -0,0 +1,134 @@
+Metadata-Version: 2.4
+Name: biolmai
+Version: 0.2.5
+Summary: BioLM Python client
+Home-page: https://github.com/BioLM/py-biolm
+Author: BioLM
+Author-email: BioLM <support@biolm.ai>
+License: Apache Software License 2.0
+Keywords: biolmai
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.7
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: httpx>=0.23.0
+Requires-Dist: httpcore
+Requires-Dist: Click>=6.0
+Requires-Dist: requests
+Requires-Dist: aiodns
+Requires-Dist: synchronicity>=0.5.0
+Requires-Dist: aiohttp<=3.8.6; python_version < "3.12"
+Requires-Dist: aiohttp>=3.9.0; python_version >= "3.12"
+Requires-Dist: async-lru
+Requires-Dist: aiofiles
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+========
+BioLM AI
+========
+
+
+.. image:: https://img.shields.io/pypi/v/biolmai.svg
+        :target: https://pypi.python.org/pypi/biolmai
+
+.. image:: https://api.travis-ci.com/BioLM/py-biolm.svg?branch=production
+        :target: https://travis-ci.org/github/BioLM/py-biolm
+
+.. image:: https://readthedocs.org/projects/biolm-ai/badge/?version=latest
+        :target: https://biolm-ai.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+
+
+
+Python client and SDK for `BioLM <https://biolm.ai>`_
+
+Install the package:
+
+.. code-block:: bash
+
+    pip install biolmai
+
+Basic usage:
+
+.. code-block:: python
+
+    from biolmai import biolm
+
+    # Encode a single sequence
+    result = biolm(entity="esm2-8m", action="encode", type="sequence", items="MSILVTRPSPAGEEL")
+
+    # Predict a batch of sequences
+    result = biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"])
+
+    # Write results to disk
+    biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"], output='disk', file_path="results.jsonl")
+
+Asynchronous usage:
+
+.. code-block:: python
+
+    from biolmai.client import BioLMApiClient
+    import asyncio
+
+    async def main():
+        model = BioLMApiClient("esmfold")
+        result = await model.predict(items=[{"sequence": "MDNELE"}])
+        print(result)
+
+    asyncio.run(main())
+
+Overview
+========
+
+The BioLM Python client provides a high-level, user-friendly interface for interacting with the BioLM API. It supports both synchronous and asynchronous usage, automatic batching, flexible error handling, and efficient processing of biological data.
+
+Main features:
+
+- High-level BioLM constructor for quick requests
+- Sync and async interfaces
+- Automatic or custom rate limiting/throttling
+- Schema-based batch size detection
+- Flexible input formats (single key + list, or list of dicts)
+- Low memory usage via generators
+- Flexible error handling (raise, continue, or stop on error)
+- Universal HTTP client for both sync and async
+
+Features
+========
+
+- **High-level constructor**: Instantly run an API call with a single line.
+- **Sync and async**: Use `BioLM` for sync, or `BioLMApiClient` for async.
+- **Flexible rate limiting**: Use API throttle, disable, or set your own (e.g., '1000/second').
+- **Schema-based batching**: Automatically queries API for max batch size.
+- **Flexible input**: Accepts a single key and list, or list of dicts, or list of lists for advanced batching.
+- **Low memory**: Uses generators for validation and batching.
+- **Error handling**: Raise HTTPX errors, continue on error, or stop on first error.
+- **Disk output**: Write results as JSONL to disk.
+- **Universal HTTP client**: Efficient for both sync and async.
+- **Direct access to schema and batching**: Use `BioLMApi` for advanced workflows, including `.schema()`, `.call()`, and `._batch_call_autoschema_or_manual()`.
+
+**Example endpoints and actions:**
+
+- `esm2-8m/encode`: Embedding for protein sequences.
+- `esmfold/predict`: Structure prediction for protein sequences.
+- `progen2-oas/generate`: Sequence generation from a context string.
+- `dnabert2/predict`: Masked prediction for protein sequences.
+- `ablang2/encode`: Embeddings for paired-chain antibodies.
+
+* Free software: Apache Software License 2.0
+* Documentation: https://docs.biolm.ai

biolmai-0.2.5/README.rst

@@ -0,0 +1,95 @@
+========
+BioLM AI
+========
+
+
+.. image:: https://img.shields.io/pypi/v/biolmai.svg
+        :target: https://pypi.python.org/pypi/biolmai
+
+.. image:: https://api.travis-ci.com/BioLM/py-biolm.svg?branch=production
+        :target: https://travis-ci.org/github/BioLM/py-biolm
+
+.. image:: https://readthedocs.org/projects/biolm-ai/badge/?version=latest
+        :target: https://biolm-ai.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+
+
+
+Python client and SDK for `BioLM <https://biolm.ai>`_
+
+Install the package:
+
+.. code-block:: bash
+
+    pip install biolmai
+
+Basic usage:
+
+.. code-block:: python
+
+    from biolmai import biolm
+
+    # Encode a single sequence
+    result = biolm(entity="esm2-8m", action="encode", type="sequence", items="MSILVTRPSPAGEEL")
+
+    # Predict a batch of sequences
+    result = biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"])
+
+    # Write results to disk
+    biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"], output='disk', file_path="results.jsonl")
+
+Asynchronous usage:
+
+.. code-block:: python
+
+    from biolmai.client import BioLMApiClient
+    import asyncio
+
+    async def main():
+        model = BioLMApiClient("esmfold")
+        result = await model.predict(items=[{"sequence": "MDNELE"}])
+        print(result)
+
+    asyncio.run(main())
+
+Overview
+========
+
+The BioLM Python client provides a high-level, user-friendly interface for interacting with the BioLM API. It supports both synchronous and asynchronous usage, automatic batching, flexible error handling, and efficient processing of biological data.
+
+Main features:
+
+- High-level BioLM constructor for quick requests
+- Sync and async interfaces
+- Automatic or custom rate limiting/throttling
+- Schema-based batch size detection
+- Flexible input formats (single key + list, or list of dicts)
+- Low memory usage via generators
+- Flexible error handling (raise, continue, or stop on error)
+- Universal HTTP client for both sync and async
+
+Features
+========
+
+- **High-level constructor**: Instantly run an API call with a single line.
+- **Sync and async**: Use `BioLM` for sync, or `BioLMApiClient` for async.
+- **Flexible rate limiting**: Use API throttle, disable, or set your own (e.g., '1000/second').
+- **Schema-based batching**: Automatically queries API for max batch size.
+- **Flexible input**: Accepts a single key and list, or list of dicts, or list of lists for advanced batching.
+- **Low memory**: Uses generators for validation and batching.
+- **Error handling**: Raise HTTPX errors, continue on error, or stop on first error.
+- **Disk output**: Write results as JSONL to disk.
+- **Universal HTTP client**: Efficient for both sync and async.
+- **Direct access to schema and batching**: Use `BioLMApi` for advanced workflows, including `.schema()`, `.call()`, and `._batch_call_autoschema_or_manual()`.
+
+**Example endpoints and actions:**
+
+- `esm2-8m/encode`: Embedding for protein sequences.
+- `esmfold/predict`: Structure prediction for protein sequences.
+- `progen2-oas/generate`: Sequence generation from a context string.
+- `dnabert2/predict`: Masked prediction for protein sequences.
+- `ablang2/encode`: Embeddings for paired-chain antibodies.
+
+* Free software: Apache Software License 2.0
+* Documentation: https://docs.biolm.ai

biolmai-0.2.5/biolmai/__init__.py

@@ -0,0 +1,24 @@
+"""Top-level package for BioLM AI."""
+__author__ = """Nikhil Haas"""
+__email__ = "nikhil@biolm.ai"
+__version__ = '0.2.5'
+
+from biolmai.client import BioLMApi, BioLMApiClient
+from biolmai.biolmai import BioLM
+from typing import Optional, Union, List, Any
+
+__all__ = ['biolm']
+
+
+def biolm(
+    *,
+    entity: str,
+    action: str,
+    type: Optional[str] = None,
+    items: Union[Any, List[Any]],
+    params: Optional[dict] = None,
+    api_key: Optional[str] = None,
+    **kwargs
+) -> Any:
+    """Top-level convenience function that wraps the BioLM class and returns the result."""
+    return BioLM(entity=entity, action=action, type=type, items=items, params=params, api_key=api_key, **kwargs)

{biolmai-0.2.3 → biolmai-0.2.5}/biolmai/auth.py

@@ -1,3 +1,4 @@
+import ast
 import json
 import os
 import pprint
@@ -9,6 +10,47 @@ import requests
 from biolmai.const import ACCESS_TOK_PATH, BASE_DOMAIN, GEN_TOKEN_URL, USER_BIOLM_DIR
 
 
+def parse_credentials_file(file_path):
+    """Parse credentials file, handling JSON, Python dict syntax, and mixed types.
+    
+    Returns a dict with 'access' and 'refresh' keys as strings, or None if parsing fails.
+    Uses ast.literal_eval() which is safe and only evaluates Python literals.
+    """
+    try:
+        with open(file_path, 'r') as f:
+            content = f.read().strip()
+        
+        # Try JSON first
+        try:
+            data = json.loads(content)
+        except json.JSONDecodeError:
+            # Fall back to safe Python literal evaluation for dict syntax like {access: 123, refresh: 456}
+            # ast.literal_eval() is safe - it only evaluates literals, no code execution
+            try:
+                data = ast.literal_eval(content)
+            except (ValueError, SyntaxError):
+                return None
+        
+        # Ensure we have a dictionary
+        if not isinstance(data, dict):
+            return None
+            
+        # Extract access and refresh, converting to strings
+        access = data.get("access")
+        refresh = data.get("refresh")
+        
+        # Convert to strings if they exist
+        if access is not None:
+            access = str(access)
+        if refresh is not None:
+            refresh = str(refresh)
+            
+        return {"access": access, "refresh": refresh}
+        
+    except Exception:
+        return None
+
+
 def validate_user_auth(api_token=None, access=None, refresh=None):
     """Validates an API token, to be used as 'Authorization: Token 1235abc'
     authentication method."""
@@ -61,8 +103,12 @@ def get_auth_status():
     elif os.path.exists(ACCESS_TOK_PATH):
         msg = f"Credentials file found {ACCESS_TOK_PATH}. Validating token..."
         click.echo(msg)
-        with open(ACCESS_TOK_PATH) as f:
-            access_refresh_dict = json.load(f)
+        access_refresh_dict = parse_credentials_file(ACCESS_TOK_PATH)
+        if access_refresh_dict is None:
+            click.echo(f"Error reading credentials file {ACCESS_TOK_PATH}.")
+            click.echo("The file may be corrupted or contain invalid data.")
+            click.echo("Please login again by running `biolmai login`.")
+            return
         access = access_refresh_dict.get("access")
         refresh = access_refresh_dict.get("refresh")
         resp = validate_user_auth(access=access, refresh=refresh)
@@ -156,8 +202,14 @@ def get_user_auth_header():
     if api_token:
         headers = {"Authorization": f"Token {api_token}"}
     elif os.path.exists(ACCESS_TOK_PATH):
-        with open(ACCESS_TOK_PATH) as f:
-            access_refresh_dict = json.load(f)
+        access_refresh_dict = parse_credentials_file(ACCESS_TOK_PATH)
+        if access_refresh_dict is None:
+            err = (
+                f"Error reading credentials file {ACCESS_TOK_PATH}. "
+                "The file may be corrupted or contain invalid data. "
+                "Please run `biolmai login` to re-authenticate."
+            )
+            raise AssertionError(err)
         access = access_refresh_dict.get("access")
         refresh = access_refresh_dict.get("refresh")
         headers = {

biolmai-0.2.5/biolmai.egg-info/PKG-INFO

@@ -0,0 +1,134 @@
+Metadata-Version: 2.4
+Name: biolmai
+Version: 0.2.5
+Summary: BioLM Python client
+Home-page: https://github.com/BioLM/py-biolm
+Author: BioLM
+Author-email: BioLM <support@biolm.ai>
+License: Apache Software License 2.0
+Keywords: biolmai
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.7
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: httpx>=0.23.0
+Requires-Dist: httpcore
+Requires-Dist: Click>=6.0
+Requires-Dist: requests
+Requires-Dist: aiodns
+Requires-Dist: synchronicity>=0.5.0
+Requires-Dist: aiohttp<=3.8.6; python_version < "3.12"
+Requires-Dist: aiohttp>=3.9.0; python_version >= "3.12"
+Requires-Dist: async-lru
+Requires-Dist: aiofiles
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+========
+BioLM AI
+========
+
+
+.. image:: https://img.shields.io/pypi/v/biolmai.svg
+        :target: https://pypi.python.org/pypi/biolmai
+
+.. image:: https://api.travis-ci.com/BioLM/py-biolm.svg?branch=production
+        :target: https://travis-ci.org/github/BioLM/py-biolm
+
+.. image:: https://readthedocs.org/projects/biolm-ai/badge/?version=latest
+        :target: https://biolm-ai.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+
+
+
+Python client and SDK for `BioLM <https://biolm.ai>`_
+
+Install the package:
+
+.. code-block:: bash
+
+    pip install biolmai
+
+Basic usage:
+
+.. code-block:: python
+
+    from biolmai import biolm
+
+    # Encode a single sequence
+    result = biolm(entity="esm2-8m", action="encode", type="sequence", items="MSILVTRPSPAGEEL")
+
+    # Predict a batch of sequences
+    result = biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"])
+
+    # Write results to disk
+    biolm(entity="esmfold", action="predict", type="sequence", items=["SEQ1", "SEQ2"], output='disk', file_path="results.jsonl")
+
+Asynchronous usage:
+
+.. code-block:: python
+
+    from biolmai.client import BioLMApiClient
+    import asyncio
+
+    async def main():
+        model = BioLMApiClient("esmfold")
+        result = await model.predict(items=[{"sequence": "MDNELE"}])
+        print(result)
+
+    asyncio.run(main())
+
+Overview
+========
+
+The BioLM Python client provides a high-level, user-friendly interface for interacting with the BioLM API. It supports both synchronous and asynchronous usage, automatic batching, flexible error handling, and efficient processing of biological data.
+
+Main features:
+
+- High-level BioLM constructor for quick requests
+- Sync and async interfaces
+- Automatic or custom rate limiting/throttling
+- Schema-based batch size detection
+- Flexible input formats (single key + list, or list of dicts)
+- Low memory usage via generators
+- Flexible error handling (raise, continue, or stop on error)
+- Universal HTTP client for both sync and async
+
+Features
+========
+
+- **High-level constructor**: Instantly run an API call with a single line.
+- **Sync and async**: Use `BioLM` for sync, or `BioLMApiClient` for async.
+- **Flexible rate limiting**: Use API throttle, disable, or set your own (e.g., '1000/second').
+- **Schema-based batching**: Automatically queries API for max batch size.
+- **Flexible input**: Accepts a single key and list, or list of dicts, or list of lists for advanced batching.
+- **Low memory**: Uses generators for validation and batching.
+- **Error handling**: Raise HTTPX errors, continue on error, or stop on first error.
+- **Disk output**: Write results as JSONL to disk.
+- **Universal HTTP client**: Efficient for both sync and async.
+- **Direct access to schema and batching**: Use `BioLMApi` for advanced workflows, including `.schema()`, `.call()`, and `._batch_call_autoschema_or_manual()`.
+
+**Example endpoints and actions:**
+
+- `esm2-8m/encode`: Embedding for protein sequences.
+- `esmfold/predict`: Structure prediction for protein sequences.
+- `progen2-oas/generate`: Sequence generation from a context string.
+- `dnabert2/predict`: Masked prediction for protein sequences.
+- `ablang2/encode`: Embeddings for paired-chain antibodies.
+
+* Free software: Apache Software License 2.0
+* Documentation: https://docs.biolm.ai

{biolmai-0.2.3 → biolmai-0.2.5}/biolmai.egg-info/SOURCES.txt

@@ -42,40 +42,6 @@ docs/_static/jupyter_notebooks_icon.png
 docs/_static/model_docs_icon.png
 docs/_static/python_sdk_icon.png
 docs/_static/tutorials_icon.png
-docs/model-docs/index.rst
-docs/model-docs/ablang/AbLang_API.rst
-docs/model-docs/ablang/AbLang_Additional.rst
-docs/model-docs/ablang/index.rst
-docs/model-docs/biolmtox/BioLMTox_API.rst
-docs/model-docs/biolmtox/BioLMTox_Additional.rst
-docs/model-docs/biolmtox/index.rst
-docs/model-docs/dnabert/DNABERT_Additional.rst
-docs/model-docs/dnabert/classifier_ft.rst
-docs/model-docs/dnabert/index.rst
-docs/model-docs/esm1v/ESM-1v_API.rst
-docs/model-docs/esm1v/ESM-1v_Additional.rst
-docs/model-docs/esm1v/index.rst
-docs/model-docs/esm2/ESM2_API.rst
-docs/model-docs/esm2/ESM2_Additional.rst
-docs/model-docs/esm2/index.rst
-docs/model-docs/esmfold/ESMFold_API.rst
-docs/model-docs/esmfold/ESMFold_Additional.rst
-docs/model-docs/esmfold/index.rst
-docs/model-docs/esmif/ESM_InverseFold_API.rst
-docs/model-docs/esmif/ESM_InverseFold_Additional.rst
-docs/model-docs/esmif/index.rst
-docs/model-docs/finetuning/index.rst
-docs/model-docs/img/book_icon.png
-docs/model-docs/img/esmfold_perf.png
-docs/model-docs/progen2/ProGen2_API.rst
-docs/model-docs/progen2/ProGen2_Additional.rst
-docs/model-docs/progen2/index.rst
-docs/model-docs/proteinfer/ProteInfer_API.rst
-docs/model-docs/proteinfer/ProteInfer_Additional.rst
-docs/model-docs/proteinfer/index.rst
-docs/model-docs/protgpt2/ProtGPT2.rst
-docs/model-docs/protgpt2/generator_ft.rst
-docs/model-docs/protgpt2/index.rst
 docs/python-client/api_biolm.rst
 docs/python-client/api_client.rst
 docs/python-client/async_sync.rst

{biolmai-0.2.3 → biolmai-0.2.5}/docs/conf.py

@@ -61,7 +61,7 @@ author = "Nikhil Haas"
 # the built documents.
 #
 # The short X.Y version.
-version = '0.2.3'
+version = '0.2.5'
 # The full version, including alpha/beta/rc tags.
 release = version
 
@@ -80,6 +80,9 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
 
+# Dark mode syntax highlighting (Furo-specific)
+pygments_dark_style = "material"
+
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
@@ -98,8 +101,58 @@ html_theme = "furo"
 html_theme_options = {
     "top_of_page_button": None,
     "sidebar_hide_name": True,
-    "light_logo": "biolm_logomark_transparent.png",
-    "dark_logo": "biolm_logomark_transparent_for_dark.png",
+    "light_logo": "biolm_logo_light.svg",
+    "dark_logo": "biolm_logo_dark.svg",
+    
+    # Custom CSS variables for branding
+    "light_css_variables": {
+        # Primary brand colors - replace with your website's brand colors
+        "color-brand-primary": "#2563eb",  # Replace with your main brand color
+        "color-brand-content": "#2563eb",  # Links and interactive elements
+        
+        # Sidebar customization
+        "color-sidebar-brand-text": "#1f2937",
+        "color-sidebar-background": "#f8fafc",
+        "color-sidebar-background-border": "#e2e8f0",
+        
+        # Additional brand colors
+        "color-admonition-title-background--note": "#dbeafe",
+        "color-admonition-title--note": "#1e40af",
+        
+        # Header and navigation
+        "color-header-background": "#ffffff",
+        "color-header-text": "#1f2937",
+        
+        # Code blocks
+        "color-code-background": "#f1f5f9",
+        "color-code-foreground": "#334155",
+        
+        # Font families to match your website exactly
+        "font-stack": '"Inter", ui-sans-serif, system-ui, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji"',
+        "font-stack--monospace": '"Roboto Mono", ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace',
+    },
+    
+    "dark_css_variables": {
+        # Dark mode brand colors
+        "color-brand-primary": "#60a5fa",  # Lighter version for dark mode
+        "color-brand-content": "#60a5fa",
+        
+        # Dark sidebar
+        "color-sidebar-background": "#1e293b",
+        "color-sidebar-background-border": "#334155",
+        "color-sidebar-brand-text": "#f1f5f9",
+        
+        # Dark mode code blocks
+        "color-code-background": "#1e293b",
+        "color-code-foreground": "#e2e8f0",
+        
+        # Additional dark mode styling
+        "color-highlight-on-target": "#374151",
+        
+        # Font families to match your website exactly (same as light mode)
+        "font-stack": '"Inter", ui-sans-serif, system-ui, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji"',
+        "font-stack--monospace": '"Roboto Mono", ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace',
+    },
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -107,6 +160,53 @@ html_theme_options = {
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
+# Custom CSS files
+html_css_files = [
+    'custom.css',
+]
+
+# Add Google Fonts (Inter and Roboto Mono to match website)
+html_css_files.extend([
+    'https://fonts.googleapis.com/css2?family=Inter:wght@100;200;300;400;500;600;700;800;900&display=swap',
+    'https://fonts.googleapis.com/css2?family=Roboto+Mono:wght@300;400;500;600;700&display=swap',
+])
+
+# Additional branding options
+html_title = "BioLM AI Documentation"
+html_short_title = "BioLM AI"
+
+# Custom favicon (add your favicon.ico to _static folder)
+# html_favicon = "_static/favicon.ico"
+
+# Custom footer
+html_show_sphinx = False
+html_show_copyright = True
+
+# SEO and metadata
+html_meta = {
+    "description": "Official documentation for BioLM AI - Advanced biological language models and APIs",
+    "keywords": "BioLM, AI, machine learning, biology, protein, DNA, API",
+    "author": "BioLM.ai Team",
+    "viewport": "width=device-width, initial-scale=1",
+}
+
+# Social media cards / Open Graph
+html_theme_options.update({
+    "announcement": None,  # Add site-wide announcements here if needed
+    "footer_icons": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/yourusername/yourrepo",  # Update with your GitHub
+            "html": """
+                <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
+                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
+                </svg>
+            """,
+            "class": "",
+        },
+    ],
+})
+
 
 # -- Options for HTMLHelp output ---------------------------------------
 

{biolmai-0.2.3 → biolmai-0.2.5}/docs/index.rst

@@ -45,20 +45,4 @@ Welcome to Our Python Client Docs
 
    tutorials_use_cases/notebooks
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Documentation:
-   :hidden:
-
-   model-docs/esm2/index
-   model-docs/esm1v/index
-   model-docs/esmfold/index
-   model-docs/esmif/index
-   model-docs/biolmtox/index
-   model-docs/progen2/index
-   model-docs/ablang/index
-   model-docs/proteinfer/index
-   model-docs/protgpt2/index
-   model-docs/dnabert/index
-   model-docs/finetuning/index
 

{biolmai-0.2.3 → biolmai-0.2.5}/docs/python-client/api_biolm.rst

@@ -34,13 +34,13 @@ A universal, high-level client for the BioLM API. Instantiating this class immed
 .. code-block:: python
 
     # ESM2-8M: encode a single sequence
-    result = BioLM(entity="esm2-8m", action="encode", type="sequence", items="MSILVTRPSPAGEEL")
+    result = biolm(entity="esm2-8m", action="encode", type="sequence", items="MSILVTRPSPAGEEL")
 
     # ESMFold: predict structure for a batch
-    result = BioLM(entity="esmfold", action="predict", type="sequence", items=["MDNELE", "MENDEL"])
+    result = biolm(entity="esmfold", action="predict", type="sequence", items=["MDNELE", "MENDEL"])
 
     # ProGen2-OAS: generate new sequences
-    result = BioLM(
+    result = biolm(
         entity="progen2-oas",
         action="generate",
         type="context",